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PubMed2006

Relationship between seed bank expression, adult longevity and aridity in species of Chaetanthera (Asteraceae) in central Chile.

BACKGROUND AND AIMS: Broad surveys have detected inverse relationships between seed and adult longevity and between seed size and adult longevity. However, low and unpredictable precipitation is also associated with seed bank (SB) expression in semi-arid and arid areas. The relationship between adult longevity, SB formation, seed mass and aridity is examined in annual and perennial herbs of Chaetanthera (Asteraceae) from the Chilean Mediterranean-type climate and winter-rainfall desert areas over a precipitation range of one order of magnitude. METHODS: Seeds of 18 species and subtaxa (32 populations) were buried in field locations, and exhumed after two successive germination periods. Seeds not germinating in the field were tested in a growth chamber, and remnant intact seed tested for viability. Seed banks were classed as transient or persistent. The effect of life form, species, population and burial time on persistent SB size was assessed with factorial ANOVA. Persistent seed bank size was compared with the Martonne aridity index (shown to be a surrogate for inter-annual variation in precipitation) and seed size using linear regression. ANCOVA assessed the effect of life-form on SB size with aridity as covariate. KEY RESULTS: Three species had a transient SB and 15 a persistent SB. ANOVA revealed a significant effect of life-form on SB size with annuals having larger SB size and greater capacity to form a persistent SB than perennials. Significant inter-population variation in SB size was found in 64% of cases. Seed mass was negatively correlated with persistent SB size. Persistent seed bank size was significantly correlated with the Martonne aridity index in the perennial and annual species, with species from more arid areas having larger persistent SBs. However, when aridity was considered as a covariate, ANCOVA revealed no significant differences between the annual and perennial herbs. CONCLUSIONS: Persistent seed bank size in Chaetanthera appears to reflect environmental selection rather than any trade-off with adult longevity.

Asteraceae↗

PubMed2005

DNA-binding properties of ARID family proteins.

The ARID (A-T Rich Interaction Domain) is a helix-turn-helix motif-based DNA-binding domain, conserved in all eukaryotes and diagnostic of a family that includes 15 distinct human proteins with important roles in development, tissue-specific gene expression and proliferation control. The 15 human ARID family proteins can be divided into seven subfamilies based on the degree of sequence identity between individual members. Most ARID family members have not been characterized with respect to their DNA-binding behavior, but it is already apparent that not all ARIDs conform to the pattern of binding AT-rich sequences. To understand better the divergent characteristics of the ARID proteins, we undertook a survey of DNA-binding properties across the entire ARID family. The results indicate that the majority of ARID subfamilies (i.e. five out of seven) bind DNA without obvious sequence preference. DNA-binding affinity also varies somewhat between subfamilies. Site-specific mutagenesis does not support suggestions made from structure analysis that specific amino acids in Loop 2 or Helix 5 are the main determinants of sequence specificity. Most probably, this is determined by multiple interacting differences across the entire ARID structure.

Amino Acid Sequence↗

PubMed2002

[Effect of arid climate on underground growth of Bothrichloa ischaemum community].

The underground growth of Bothrichloa ischaemum community in extremely arid year were compared with that of the community in 1991 with normal precipitation, and hence, could reflect the effect of drought on underground growth of Bothrichloa ischaemum community. The results indicated that the peak value of underground biomass reached 1249 g.m-2 in extremely arid year, higher than that in normal year (586 g.m-2). Most roots distributed downwards in extremely arid year or arid seasons, and distributed upwards in normal year or rain seasons. The turnover rate of underground biomass in extremely arid year was 52.64%, significantly higher than that in normal year (18.36%). In extremely arid year, underground part and aboveground part competed with each other at the middle and later stage of growth, however, in normal year, they increased simultaneously presenting beeline correlativity on the whole. The biomass ratio of underground to aboveground in extremely arid year was 11.19 and significantly higher than that in normal year (2.03). Net underground primary production in extremely arid year was 390.7 g.m-2.yr.-1 and 2.63 times higher than that in normal year.

Climate↗

PubMed2005

Nomenclature of the ARID family of DNA-binding proteins.

The ARID is an ancient DNA-binding domain that is conserved throughout the evolution of higher eukaryotes. The ARID consensus sequence spans about 100 amino acid residues, and structural studies identify the major groove contact site as a modified helix-turn-helix motif. ARID-containing proteins exhibit a range of cellular functions, including participation in chromatin remodeling, and regulation of gene expression during cell growth, differentiation, and development. A subset of ARID family proteins binds DNA specifically at AT-rich sites; the remainder bind DNA nonspecifically. Orthologs to each of the seven distinct subfamilies of mammalian ARID-containing proteins are found in insect genomes, indicating the minimum age for the organization of these higher metazoan subfamilies. Many of these ancestral genes were duplicated and fixed over time to yield the 15 ARID-containing genes that are found in the human, mouse, and dog genomes. This paper describes a nomenclature, recommended by the Mouse Genomic Nomenclature Committee (MGNC) and accepted by the Human Genome Organization (HUGO) Gene Nomenclature Committee, for these mammalian ARID-containing genes that reflects this evolutionary history.

Amino Acid Sequence↗

PubMed2002

The structure of the Dead ringer-DNA complex reveals how AT-rich interaction domains (ARIDs) recognize DNA.

The AT-rich interaction domain (ARID) is a DNA-binding module found in many eukaryotic transcription factors. Using NMR spectroscopy, we have determined the first ever three-dimensional structure of an ARID--DNA complex (mol. wt 25.7 kDa) formed by Dead ringer from Drosophila melanogaster. ARIDs recognize DNA through a novel mechanism involving major groove immobilization of a large loop that connects the helices of a non-canonical helix-turn-helix motif, and through a concomitant structural rearrangement that produces stabilizing contacts from a beta-hairpin. Dead ringer's preference for AT-rich DNA originates from three positions within the ARID fold that form energetically significant contacts to an adenine-thymine base step. Amino acids that dictate binding specificity are not highly conserved, suggesting that ARIDs will bind to a range of nucleotide sequences. Extended ARIDs, found in several sequence-specific transcription factors, are distinguished by the presence of a C-terminal helix that may increase their intrinsic affinity for DNA. The prevalence of serine amino acids at all specificity determining positions suggests that ARIDs within SWI/SNF-related complexes will interact with DNA non-sequence specifically.

Adenine↗

PubMed2004

The DNA-binding properties of the ARID-containing subunits of yeast and mammalian SWI/SNF complexes.

SWI/SNF complexes are ATP-dependent chromatin remodeling complexes that are highly conserved from yeast to human. From yeast to human the complexes contain a subunit with an ARID (A-T-rich interaction domain) DNA-binding domain. In yeast this subunit is SWI1 and in human there are two closely related alternative subunits, p270 and ARID1B. We describe here a comparison of the DNA-binding properties of the yeast and human SWI/SNF ARID-containing subunits. We have determined that SWI1 is an unusual member of the ARID family in both its ARID sequence and in the fact that its DNA-binding affinity is weaker than that of other ARID family members, including its human counterparts, p270 and ARID1B. Sequence analysis and substitution mutagenesis reveals that the weak DNA-binding affinity of the SWI1 ARID is an intrinsic feature of its sequence, arising from specific variations in the major groove interaction site. In addition, this work confirms the finding that p270 binds DNA without regard to sequence specificity, excluding the possibility that the intrinsic role of the ARID is to recruit SWI/SNF complexes to specific promoter sequences. These results emphasize that care must be taken when comparing yeast and higher eukaryotic SWI/SNF complexes in terms of DNA-binding mechanisms.

Amino Acid Sequence↗

PubMed2002

ARID proteins: a diverse family of DNA binding proteins implicated in the control of cell growth, differentiation, and development.

The ARID family of DNA binding proteins was first recognized approximately 5 years ago. The founding members, murine Bright and Drosophila dead ringer (Dri), were independently cloned on the basis of their ability to bind to AT-rich DNA sequences, although neither cDNA encoded a recognizable DNA binding domain. Mapping of the respective binding activities revealed a shared but previously unrecognized DNA binding domain, the consensus sequence of which extends across approximately 100 amino acids. This novel DNA binding domain was designated AT-rich interactive domain (ARID), based on the behavior of Bright and Dri. The consensus sequence occurs in 13 distinct human proteins and in proteins from all sequenced eukaryotic organisms. The majority of ARID-containing proteins were not cloned in the context of DNA binding activity, however, and their features as DNA binding proteins are only beginning to be investigated. The ARID region itself shows more diversity in structure and function than the highly conserved consensus sequence suggests. The basic structure appears to be a series of six alpha-helices separated by beta-strands, loops, or turns, but the structured region may extend to an additional helix at either or both ends of the basic six. It has also become apparent that the DNA binding activity of ARID-containing proteins is not necessarily sequence specific. What is consistent is the evidence that family members play vital roles in the regulation of development and/or tissue-specific gene expression. Inappropriate expression of ARID proteins is also increasingly implicated in human tumorigenesis. This review summarizes current knowledge about the structure and function of ARID family members, with a particular focus on the human proteins.

AT Rich Sequence↗

PubMed2002

The Drosophila retained/dead ringer gene and ARID gene family function during development.

The recently discovered ARID family of proteins interact with DNA through a phylogenetically conserved sequence termed the A/T Interaction Domain (ARID). The retained/dead ringer (retn/dri) gene of Drosophila melanogaster is a founding member of the ARID gene family, and of the eARID subfamily. This subfamily exhibits an extended region of sequence similarity beyond the core ARID motif and a separate conserved domain termed the REKLES domain. retn/dri is involved in a range of developmental processes, including axis patterning and muscle development. The retn/dri ARID motif has been shown by in vitro studies to exhibit sequence-specific DNA binding activity. Here we demonstrate that the ARID domain is essential for the in vivo function of retn/dri during embryonic development by showing that a mutant form of RETN/DRI, deleted for part of the ARID domain and unable to bind DNA in vitro, cannot rescue the retn/dri mutant phenotype. In the presence of wild-type RETN/DRI this construct acts as a dominant negative, providing additional support for the proposal that RETN/DRI acts in a multiprotein complex. In contrast, we are yet to find an in vivo role for the REKLES domain, despite its clear evolutionary conservation. Finally, we have used germline clone analysis to reveal a requirement for retn/dri in the Drosophila preblastoderm syncytial mitoses.

Amino Acid Motifs↗

PubMed2003

Adaptation of metabolism and evaporative water loss along an aridity gradient.

Broad-scale comparisons of birds indicate the possibility of adaptive modification of basal metabolic rate (BMR) and total evaporative water loss (TEWL) in species from desert environments, but these might be confounded by phylogeny or phenotypic plasticity. This study relates variation in avian BMR and TEWL to a continuously varying measure of environment, aridity. We test the hypotheses that BMR and TEWL are reduced along an aridity gradient within the lark family (Alaudidae), and investigate the role of phylogenetic inertia. For 12 species of lark, BMR and TEWL decreased along a gradient of increasing aridity, a finding consistent with our proposals. We constructed a phylogeny for 22 species of lark based on sequences of two mitochondrial genes, and investigated whether phylogenetic affinity played a part in the correlation of phenotype and environment. A test for serial independence of the data for mass-corrected TEWL and aridity showed no influence of phylogeny on our findings. However, we did discover a significant phylogenetic effect in mass-corrected data for BMR, a result attributable to common phylogenetic history or to common ecological factors. A test of the relationship between BMR and aridity using phylogenetic independent constrasts was consistent with our previous analysis: BMR decreased with increasing aridity.

Adaptation, Physiological↗

PubMed2001

Genomic dissection of genotype x environment interactions conferring adaptation of cotton to arid conditions.

The interaction of genotype with environment is of primary importance in many aspects of genomic research and is a special priority in the study of major crops grown in a wide range of environments. Water deficit, the major factor limiting plant growth and crop productivity worldwide, is expected to increase with the spread of arid lands. In genetically equivalent cotton populations grown under well-watered and water-limited conditions (the latter is responsible for yield reduction of approximately 50% relative to well-watered conditions), productivity and quality were shown to be partly accounted for by different quantitative trait loci (QTLs), indicating that adaptation to both arid and favorable conditions can be combined in the same genotype. QTL mapping was also used to test the association between productivity and quality under water deficit with a suite of traits often found to differ between genotypes adapted to arid versus well-watered conditions. In this study, only reduced plant osmotic potential was clearly implicated in improved cotton productivity under arid conditions. Genomic tools and approaches may expedite breeding of genotypes that respond favorably to specific environments, help test roles of additional physiological factors, and guide the isolation of genes that protect crop performance under arid conditions toward improved adaptation of crops to arid cultivation.

Adaptation, Physiological↗

PubMed2000

The human SWI-SNF complex protein p270 is an ARID family member with non-sequence-specific DNA binding activity.

p270 is an integral member of human SWI-SNF complexes, first identified through its shared antigenic specificity with p300 and CREB binding protein. The deduced amino acid sequence of p270 reported here indicates that it is a member of an evolutionarily conserved family of proteins distinguished by the presence of a DNA binding motif termed ARID (AT-rich interactive domain). The ARID consensus and other structural features are common to both p270 and yeast SWI1, suggesting that p270 is a human counterpart of SWI1. The approximately 100-residue ARID sequence is present in a series of proteins strongly implicated in the regulation of cell growth, development, and tissue-specific gene expression. Although about a dozen ARID proteins can be identified from database searches, to date, only Bright (a regulator of B-cell-specific gene expression), dead ringer (a Drosophila melanogaster gene product required for normal development), and MRF-2 (which represses expression from the cytomegalovirus enhancer) have been analyzed directly in regard to their DNA binding properties. Each binds preferentially to AT-rich sites. In contrast, p270 shows no sequence preference in its DNA binding activity, thereby demonstrating that AT-rich binding is not an intrinsic property of ARID domains and that ARID family proteins may be involved in a wider range of DNA interactions.

Amino Acid Sequence↗

PubMed1992

A stereological analysis of kidney structure of honeyeater birds (Meliphagidae) inhabiting either arid or wet environments.

Stereology was used to quantify components within the kidney of honeyeater birds. Arid zone and wet zone inhabiting 'matched' body mass pairs of birds were examined. The kidney structure of the arid zone white-fronted honeyeater, Phylidonyris albifrons (16.9 g), was compared with that of the wet zone New Holland honeyeater, Phylidonyris novaehollandiae (21.9 g), and that of the arid zone spiny-cheeked honeyeater, Acanthogenys rufogularis (42.5 g), with that of the wet zone little wattlebird, Anthochaera lunulata (62.0 g). Both arid zone honeyeaters had a significantly higher (P less than 0.001) percentage of medulla in the kidneys, while the wet zone birds had a significantly higher (P less than 0.001) percentage of cortex. There were few differences between arid and wet zone honeyeaters in the percentage of nephron components in the cortex and medulla. Both arid zone bird species had a significantly larger volume of medulla, a feature characteristic of a high ability to conserve water by producing a concentrated urine. Both wet zone species had a higher volume of cortex but the difference was not significant. Few differences were found in the volumes and surface areas of tubules within the nephron. Differences that did occur were not always consistent with a high ability to conserve either ions or water more efficiently. The volume and surface area of brush border in the proximal tubule were significantly higher in the little wattlebird. This characteristic may lead to a greater capacity of its kidneys to absorb both water and ions.

Animals↗

PubMed2025

Multiomic Analyses Reveal the Molecular Mechanisms of Arid Adaptation in a Desert Rodent Species.

Organisms living in desert habitats face multiple simultaneous pressures, such as high temperatures and arid, and the population dynamics and community diversity of small rodents are strongly affected by climate extremes. However, the potential mechanisms by which desert rodents adapt to arid remain largely unexplored. Here, we assembled a 3.18 Gb genome, including 25,812 protein-encoding genes, for Orientallactaga sibirica, which is widely distributed across both arid and semihumid environments in Eurasia. Orientallactaga sibirica has longer ears and hind limbs to enhance heat dissipation, which may be related to the positively selected genes, such as Fgf10, Fgf11, Hoxc4, Hoxd1, and Bmp4. The renal transcriptome revealed increased fat and carbohydrate metabolism for metabolic water production in O. sibirica residing in arid habitats. Pathways such as material metabolism, oxidative stress response, osmoregulation, and water and salt reabsorption were enriched in candidate genes, such as Avp, Ang, and Ace, under positive selection in O. sibirica. Moreover, amino acid replacement was observed in the protein sequences of seven candidate genes, including Aldh7a1, Lnpep, Wnk4, C1qc, and Awat2, and these specific amino acid replacements of genes such as Umod and Scnn1a were related to unique osmoregulation, osmotic protection, and water retention compensation mechanisms. Water deprivation under laboratory conditions induced the upregulation of Umod and Aldh7a1 expression, further supporting the results observed in the wild population. These findings demonstrate that the positively selected genes related to limb development and specific amino acid replacements in the genes Umod and Scnn1a for unique osmoregulation in the renal vascular system may contribute to arid adaptation in the desert rodent species O. sibirica. This study provides novel insights into the adaptive evolution of desert small mammals and can serve as a reference for future research on renal damage-related diseases, such as human kidney stones and salt-sensitive hypertension.

Animals↗

PubMed2003

Sperm motion characteristics of Garole rams raised for a prolonged period in a semi-arid tropical environment.

The Garole is a prolific but less well known and rare breed of small sheep found in the hot and humid Sunderban region of West Bengal. An ability to breed throughout the year and to graze in knee-deep water, resistance to foot rot and a strong mothering instinct are some of the special features of this breed. Garole rams could provide germplasm to incorporate prolificacy traits by artificial insemination of the nonprolific sheep breeds found in abundance in the semi-arid and arid tropical climates of India. The aim of the present study was to evaluate the semen production by Garole rams maintained in a semi-arid climate for three years and to objectively assess their semen quality by a computer-assisted sperm analysis technique. The donor rams were randomly selected each year from the original flock procured from their natural habitat or from the offspring born at the Institute farm. Semen was collected weekly for three weeks each autumn for three consecutive years from 8 rams each year. The overall means (SD) of the traits that did not differ significantly with age or year were volume, concentration, curvilinear velocity, average path velocity, amplitude of lateral head displacement, beat frequency, motility and the percentages of rapid motile sperms and of slow motile sperms. The age of the rams had a significant effect (p<0.05) on the straight-line velocity but this was not significantly affected by the length of exposure to the semi-arid climate. However, the age and year had significant effects (p<0.05) on linearity, straightness and the percentage of medium motile sperms. It was concluded that Garole rams are capable of producing good-quality semen even after a prolonged period of exposure to a semi-arid tropical climate.

Animals↗

PubMed2006

A stable isotope aridity index for terrestrial environments.

We use the oxygen isotopic composition of tooth enamel from multiple mammalian taxa across eastern Africa to present a proxy for aridity. Here we report tooth enamel delta(18)O values of 14 species from 18 locations and classify them according to their isotopic sensitivity to environmental aridity. The species are placed into two groups, evaporation sensitive (ES) and evaporation insensitive (EI). Tooth enamel delta(18)O values of ES animals increase with aridity, whereas the tooth enamel delta(18)O values of EI animals track local meteoric water delta(18)O values, demonstrating that bioapatite delta(18)O values of animals with different behaviors and physiologies record different aspects of the same environment. The enrichment between tooth enamel delta(18)O values of ES and EI animals records the degree of (18)O enrichment between evaporated water (ingested water or body water) and source water, which increases with environmental aridity. Recognition of the ES-EI distinction creates the opportunity to use the (18)O composition of bioapatite as an index of terrestrial aridity.

Animals↗

PubMed2003

Variation in onset of summer dormancy and flowering capacity along an aridity gradient in Poa bulbosa L., a geophytic perennial grass.

Variation in the onset of summer dormancy and flowering capacity of 16 populations of Poa bulbosa, collected along a steep north-south aridity gradient in Israel (810-110 mm rain year(-1)), was studied under controlled conditions in a phytotron (16 h daylength, 22/16 degrees C day/night) and under natural conditions in a garden experiment in a net-house. Plant age at the onset of dormancy varied markedly amongst populations (7-16 weeks under controlled conditions) and was positively correlated with mean annual precipitation at the site of origin of the population, i.e. dormancy was earlier as aridity increased. Flowering capacity in the different populations was negatively correlated with rainfall in the original habitat and, consequently, also with the age at onset of dormancy, i.e. the lower the mean annual precipitation, the earlier the onset of dormancy and the higher the proportion of flowering plants and panicles per plant. Differences in xeromorphic leaf traits were also observed among populations from locations differing in aridity. Plants from the more arid sites (110-310 mm year(-1)) generally had greyish and curved leaves, whereas plants from more humid sites (500-810 mm year(-1)) tended to have green and straight leaves. Thus, plants with curved and/or greyish leaves generally had a higher flowering capacity and entered dormancy earlier than plants with straight and/or green leaves. The significance of the association among these traits for the adaptation of P. bulbosa to increasing aridity is discussed.

Adaptation, Physiological↗

PubMed2000

The Effects of Irrigation on Revegetation of Semi-Arid Coastal Sage Scrub in Southern California.

/ To test the appropriateness and applicability of irrigation for restoration of coastal sage scrub, a semi-arid vegetation type native to southern California, a field study comparing four irrigation schedules-no irrigation, spring irrigation only, summer irrigation only, and irrigation year round as needed-was established. A seed mixture of six native shrub species was broadcast, and the effect of irrigation on emergence and establishment was evaluated. Restoration of arid and semi-arid vegetation is challenging because of the severe environmental conditions inherent to these ecosystems. In particular, the low and unpredictable nature of precipitation can limit the chances for successful establishment of perennial species. Under conditions where supplemental irrigation is available, irrigation may make the difference between successful or failed restoration. However, increasing the availability of water through irrigation may result in poor plant adaptation to surviving arid conditions or only temporary success followed by failure once supplemental water is withdrawn. In this study, irrigation stimulated germination in the irrigated plots about a month earlier than the plots dependent on natural rainfall, but this had little lasting effect. Spring and summer irrigation did not improve survival compared to the plots receiving no supplemental water. The largest effect of irrigation was a reduction in survival of several species grown under irrigated conditions as compared to nonirrigated conditions. In plots where water was applied all year long a single species, Artemisia californica, represented nearly 100% of the species present at the end of two growing seasons. Irrigation may speed revegetation under some conditions, but was not very effective in establishing natural vegetation structure.

Journal Article↗

PubMed2001

Erythrocyte osmotic fragility of red (Macropus rufus) and grey (Macropus fuliginosus and Macropus giganteus) kangaroos and free-ranging sheep of the arid regions of Australia.

The mean corpuscular fragility (MCF) of erythrocytes may reflect phylogenetic characteristics as well as an animal's ability to respond to the osmotic challenges associated with cyclic dehydration and rehydration. This type of ecophysiological stress is commonly encountered by animals living in arid regions and low MCF may contribute to their ability to survive and thrive in these xeric habitats. The eastern grey kangaroo has only in recent times extended its range into the arid zone, and is considered a more mesic inhabitant than the red kangaroo. We therefore compared the ability of eastern grey kangaroos and red kangaroos to handle prolonged periods of water restriction, as well as the MCF of the erythrocytes of free-ranging red, eastern grey and western grey kangaroos found at the Fowlers Gap field station. In addition, the MCF of free-ranging sheep inhabiting the same pastures were used as an experimental control; they are phylogenetically unrelated yet are subjected to the same acclimatisation stresses. While red kangaroos exhibited greater tolerance of dehydration compared to eastern grey kangaroos, the MCF of all three kangaroo species was similar and more resilient to osmotic stresses (MCF, 130 mosmol/kg) than erythrocytes of sheep (MCF, 220 mosmol/kg). The MCF did not change with water restriction, however, the erythrocytes of long-term captive populations fed a comparatively better quality diet were more resistant to osmotic shock than the free-ranging animals. Phylogenetic commonality rather than ecophysiological responses to life in the arid zone appeared to influence MCF. The MCF values of sheep corresponded to that of other ovines; similarly the MCF of kangaroos concurred regardless of their preferred habitats. ecological history and differential success in the arid zone.

Animals↗