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PubMed1991

Draft results of a workshop to develop guidelines for studies involving microbial incidence or populations in the oral cavity.

The following five outlines are the results to date of the Workshop held in Rockville, Maryland, in January, 1990. The topics considered in these outlines are: (1) validation of immunological and/or nucleic acid identification probes, (2) cross-calibration of methods and/or laboratories for multi-laboratory cooperative studies, (3) choosing methods for identifying or describing microbial populations appropriate to the scientific question asked, (4) microbial ecology methods (e.g., population dynamics) for the oral cavity studies, and (5) epidemiological methods (e.g., incidence, risk factor analysis) for oral microbial studies. Each topic was considered by two independent groups of participants and later rationalized into one. These outlines are meant to be working outlines for evolution of a set of guidelines to advise on designing studies with microbial incidence and/or population components. We are publishing this preliminary version to elicit comment and criticism from people who did not attend the Workshop. (Attendance at the Workshop was necessarily limited by both space and funds). Some of the topic outlines have been condensed to save Journal space. The full document is available on request. The next stage will be an open forum to gather and discuss further amplification of the "Guidelines", planned for April 17, 1991, Acapulco, Mexico, in conjunction with the IADR/AADR Meeting. Written comments and requests for further information should be sent to the Workshop organizer (MIK) at the above address.(ABSTRACT TRUNCATED AT 250 WORDS)

DNA, Bacterial↗
PubMed2026

Host-driven evolution shapes the polysaccharide utilization profiles of alga-associated Flavobacteriaceae.

BACKGROUND: Marine algae represent major producers of complex polysaccharides and serve as hosts for diverse microbial communities in the phycosphere. Flavobacteriaceae are among the key bacterial taxa involved in polysaccharide degradation and carbon remineralization in this environment. However, the extent to which algal hosts drive the divergence of polysaccharide utilization profiles in these bacteria remains unclear. RESULTS: We conducted a genome-resolved analysis of 103 cultured Flavobacteriaceae strains isolated from red, green, and brown macroalgae, as well as from diatoms and dinoflagellates. We found that macroalga-associated strains generally harbored more abundant and diverse CAZyme-encoding genes than their microalga-associated counterparts. Moreover, strains associated with different algal phyla showed distinct metabolic specializations that aligned with the typical polysaccharides of their respective hosts, strongly supporting host-specific adaptation. In four widely distributed genera (Maribacter, Flagellimonas, Polaribacter, Winogradskyella), CAZyme profile dissimilarity and key glycoside hydrolase gene divergence exhibited phylogenetic congruence with algal host phylogeny (Mantel r up to 0.76 and 0.85, respectively), indicative of host-associated functional adaptation. Using Maribacter as a model, cultivation experiments and transcriptome characterization demonstrated that polysaccharide utilization efficiency is not solely linked to the organization of genes into polysaccharide utilization loci (PULs), but also associated with the expression dynamics of key transcription factors (TFs), particularly those from AraC and DeoR families, whose expression patterns were coordinated with laminarin degradation. Notably, these two TF families also exhibited host-associated divergence patterns similar to those of CAZyme-encoding genes. Furthermore, analysis of the Tara Oceans metagenomic data indicated that, within the AraC and DeoR families, a higher proportion of genes were positively correlated with chlorophyll a content compared to other TF families, reinforcing their specialized roles in alga-associated bacterial lifestyles. CONCLUSIONS: Our integrative genomic and transcriptomic analyses reveal evolutionary and regulatory adaptation of marine Flavobacteriaceae to distinct algal hosts. These findings highlight algae-derived habitats as specialized niches that shape microbial metabolic potential, and suggest that carbohydrate metabolism plays a key role in host-driven bacterial evolution across global oceans. Video Abstract.

Flavobacteriaceae↗
PubMed2026

Concurrent ecological and evolutionary processes contribute to mutualism breakdown between legumes and rhizobia.

Though they jointly shape community responses to environmental perturbations, ecology and evolution are often examined separately, even in microorganisms where both occur over short timescales. Here we examine ecological and evolutionary responses to 33 years of nitrogen fertilization using the legume-rhizobium mutualism. Pairing a manipulative inoculation study with full-length 16S rRNA gene amplicon sequencing and structural equation modeling allows us to synthesize across biological scales: whole bacterial community, genus Rhizobium, Rhizobium ASVs, and symbiosis plasmids. Clover's preferred partner decreases in N-addition soils, limiting host growth, while a diverse and largely uncharacterized Rhizobium community increases. This ecological change is compounded by a concurrent evolutionary degradation of symbiont partner quality via changing frequencies of symbiotic plasmids. Ecological (rarer symbionts) and evolutionary (inferior symbionts) processes each accounted for roughly half of this loss of host benefit, revealing that ecology and evolution jointly shape mutualism breakdown over the short timescales typical of microbial systems.

ecology↗
PubMed1991

Human lysosomal cathepsin G and granzyme B share a functionally conserved broad spectrum antibacterial peptide.

Human neutrophil lysosomal cathepsin G (cat G) exerts broad-spectrum antibacterial action in vitro against Gram-negative and -positive bacteria independent of its serine protease activity. We recently determined that an internal peptide of cat G (HPQYNQR), obtained after digestion of cat G with clostripain, possessed broad-spectrum antibacterial action in vitro, displaying an ED50 of 5 x 10(-5) M. In order to evaluate the structure-antibacterial properties of this peptide, synthetic variants with single alanine substitutions at each position were prepared and tested for antibacterial action. We found that alanine substitution for His-1 or Tyr-4, or certain modifications of the His-1 side chain, produced nonbactericidal peptides. A hexapeptide lacking the COOH-terminal Arg-7 but not a pentapeptide lacking both Gln-6 and Arg-7 possessed in vitro bactericidal activity. Interestingly, the cat G bactericidal peptide displays similarity to sequences within other serine proteases, notably the proposed cytotoxic granzymes present in the cytolytic granules of human and mouse cytotoxic T lymphocytes. We now report that an internal peptide of one human granzyme (granzyme B) with the sequence of HPAYNPK also displays bactericidal action in vitro. Our results suggest that an internal antibacterial domain among human serine proteases cat G and granzyme B has been functionally conserved through evolution perhaps for the purpose of host defense against microbial pathogens and targets of cytotoxic T lymphocyte killing.

Amino Acid Sequence↗
PubMed1992

Microbial life at high pressures.

Deep-sea environment have selected for the evolution of unusual bacterial extremophiles which are adapted to life at high pressures. This review briefly characterises barophilic bacteria; compares and contrasts high pressure effects on cellular and biochemical processes in both barosensitive and barophilic bacteria; and presents molecular and genetic approaches which have been used to examine the basis of high pressure sensitivity in terrestrial barosensitive bacteria, or to dissect barophilic processes in deep-sea bacteria.

Air Pressure↗
PubMed1978

Microbial catabolism, the carbon cycle and environmental pollution.

The establishment of a carbon cycle was a necessary prerequisite for the evolution of higher forms of life. This could not have been achieved without the direct participation of oxygen gas in certain metabolic reactions. The controlled activation of oxygen is catalyzed by microbial oxygenases; in principle, activated oxygen is hazardous to all living forms but without it, the degradative segment of the carbon cycle could not operate. The degradation of aromatic compounds is not an esoteric activity of a few specialized microorganisms. It occurs continuously, accompanied by fixation and cycling of oxygen on a massive scale; but like other global biochemical processes it tends to be neglected in general biological curricula. However, knowledge of the scope and limitations of microbial catabolic enzymes is central to the development of rational approaches to many of society's environmental concerns.

Acinetobacter↗
PubMed1991

Origin of tetracycline efflux proteins: conclusions from nucleotide sequence analysis.

The sequences of six tetracycline efflux proteins and three transport proteins which have some resemblance to them were compared. The tetracycline efflux proteins fall into three families: (i) those encoded by pBR322, RP1, and Tn10 (Escherichia coli); (ii) pT181 (Staphylococcus aureus) and pTHT15 (Bacillus subtilis); and (iii) tet347 (Streptomyces rimosus). There is global sequence homology within each of the first two families, but there is none between the families. The pT181/pTHT15 family shares close homology with the N-terminal half of the methylenomycin A efflux protein (Streptomyces coelicor), while tet347 resembles the C-terminal half. Portions of the N-terminal half of the Tn10-encoded protein show significant resemblance to portions in the N-terminal half of the pT181/pTHT15 family, but this sometimes occurs among transport proteins which do not have a common substrate. Tetracycline efflux proteins, therefore, appear to have arisen on at least two, or possibly three, separate occasions, probably from other transport proteins.

Amino Acid Sequence↗
PubMed1987

Bacterial resistance to beta-lactam antibiotics: crystal structure of beta-lactamase from Staphylococcus aureus PC1 at 2.5 A resolution.

beta-lactamases are enzymes that protect bacteria from the lethal effects of beta-lactam antibiotics, and are therefore of considerable clinical importance. The crystal structure of beta-lactamase from the Gram-positive bacterium Staphylococcus aureus PC1 has been determined at 2.5 angstrom resolution. It reveals a molecule of novel topology, made up of two closely associated domains. The active site is located at the interface between the domains, with the key catalytic residue Ser70 at the amino terminus of a buried helix. Examination of the disposition of the functionally important residues within the active site depression leads to a model for the binding of a substrate and a functional analogy to the serine proteases. The unusual topology of the secondary structure units is relevant to questions concerning the evolutionary relation to the beta-lactam target enzymes of the bacterial cell wall.

Anti-Bacterial Agents↗
PubMed1972

Temperature-dependent utilization of meso-inositol: a useful biotyping marker in the genealogy of Salmonella typhimurium.

Salmonella typhimurium strains from natural sources either ferment or do not ferment meso-inositol in peptone water in 24 hr at 37 C. Ninety-five percent of the strains that are designated inositol-nonfermenting on the basis of their phenotype at 37 C ferment inositol when incubated at 25 C. Two classes of temperature-sensitive mutants were detected among the 712 strains of S. typhimurium examined. The occurrence of low-temperature fermentation of inositol among wild-type strains of S. typhimurium from biotypes 10 through 13 and FIRN suggested a genealogical relationship between these two groups, and that FIRN strains (fim(-)inl(ts)rha(-)) might have descended from ancestral types like biotype 10 through 13 strains (fim(+)inl(ts)rha(+)).

Biological Evolution↗
PubMed1992

Origin, structure, and regulation of argK, encoding the phaseolotoxin-resistant ornithine carbamoyltransferase in Pseudomonas syringae pv. phaseolicola, and functional expression of argK in transgenic tobacco.

Pseudomonas syringae pv. phaseolicola produces the tripeptide N delta(N'-sulfo-diaminophosphinyl)-ornithylalanyl-homoarginin e (phaseolotoxin), which functions as a chlorosis-inducing toxin in the bean halo blight disease by inhibiting ornithine carbamoyltransferase (OCT). The bacterium possesses duplicate OCT genes, one of which, argK, encodes a toxin-resistant enzyme (ROCT) and imparts resistance to phaseolotoxin. We sequenced the argK gene from strain NPS3121, defined its promoter region, analyzed its regulation, and characterized its transcripts. The gene probably originated from another organism, since it is very distantly related to the argF gene encoding the housekeeping toxin-sensitive OCT and has low G+C content compared with the bacterial genome as a whole and with other protein-coding genes from P. syringae pv. phaseolicola. Optimized alignments of 13 OCT sequences allowed us to define key residues that may be responsible for toxin resistance and to identify a distinct prokaryotic amino acid signature, in ROCT, which argues for a prokaryotic origin of argK. An in-frame fusion of the argK coding region with the chloroplast transit peptide segment of the pea rbcS gene was introduced in Nicotiana tabacum by Agrobacterium-mediated transformation. The presence of an ROCT activity in transgenic plants was demonstrated by in vitro and in vivo assays. Some plants were toxin resistant, suggesting that pathogen-derived resistance to the toxin should be feasible in the pathogen's host.

Amino Acid Sequence↗