Annual Review of Microbiology - Volume 63, 2009

Frankly, I was surprised to receive an invitation to write a prefatory chapter for the Annual Review of Microbiology. I have read several such chapters written by outstanding researchers, many of whom I know and admire. I did not think I belonged to such a preeminent group. In my view, my contributions to the physiology and biochemistry of anaerobic thermophilic bacteria and, more lately, to anaerobic fungi are modest compared to the contribution made by other authors of prefatory chapters. I am honored to write about my life and my work, and I hope that those who read this chapter will sense how exciting and rewarding they have been.

RNA binding proteins are capable of regulating translation initiation by a variety of mechanisms. Although the vast majority of these regulatory mechanisms involve translational repression, one example of translational activation has been characterized in detail. The RNA recognition targets of these regulatory proteins exhibit a wide range in structural complexity, with some proteins recognizing complex pseudoknot structures and others binding to simple RNA hairpins and/or short repeated single-stranded sequences. In some instances the bound protein directly competes with ribosome binding, and in other instances the bound protein promotes formation of an RNA structure that inhibits ribosome binding. Examples also exist in which the bound protein traps the ribosome in a complex that is incapable of initiating translation.

Bacteria sense the chemical world using a variety of mechanisms that include the frequently described two-component system (TCS), which comprises a sensor kinase and response regulator, to regulate gene expression in response to environmental cues. One of the best and most widely studied versions of the TCS is the system that controls chemotaxis in Escherichia coli. The chemotaxis machinery includes components not found in other TCS to regulate motility and is therefore an exception to the rule for two-component signaling. The hallmark feature of the chemotaxis system is the presence of an adaptation module in which the sensor receptor protein is posttranslationally modified to attenuate ligand-induced signaling, a mechanism not yet identified for the more widely distributed prototypical TCS. More recently, variations on the chemotaxis system itself have been identified and they are termed chemosensory systems and are the subject of this review. Extensive research has provided a perspective on TCS signaling and indicates that variation and diversity for the standard two-component system are predominant in the microbial world.

Translating the 4-letter code of RNA into the 22-letter alphabet of proteins is a central feature of cellular life. The fidelity with which mRNA is translated during protein synthesis is determined by two factors: the availability of aminoacyl-tRNAs composed of cognate amino acid:tRNA pairs and the accurate selection of aminoacyl-tRNAs on the ribosome. The role of aminoacyl-tRNA synthetases in translation is to define the genetic code by accurately pairing cognate tRNAs with their corresponding amino acids. Synthetases achieve the amino acid substrate specificity necessary to keep errors in translation to an acceptable level in two ways: preferential binding of the cognate amino acid and selective editing of near-cognate amino acids. Editing significantly decreases the frequency of errors and is important for translational quality control, and many details of the various editing mechanisms and their effect on different cellular systems are now starting to emerge.

Influenza viruses continue to pose a major global public health problem. There is a need to better understand the pathogenicity and transmission of pandemic influenza viruses so that we may develop improved methods for their prevention and control. Reconstruction of the 1918 virus and studies elucidating the exceptional virulence and transmissibility of the virus are providing exciting new insights into this devastating pandemic strain. The primary approach has been to reconstruct and analyze recombinant viruses, in which genes of the 1918 virus are replaced with genes of contemporary influenza viruses of lesser virulence. This review highlights the current status of the field and discusses the molecular determinants of the 1918 pandemic virus that may have contributed to its virulence and spread. Identifying the exact genes responsible for the high virulence of the 1918 virus will be an important step toward understanding virulent influenza strains and will allow the world to better prepare for and respond to future influenza pandemics.

Our view of bacteria, from the earliest observations through the heyday of antibiotic discovery, has shifted dramatically. We recognize communities of bacteria as integral and functionally important components of diverse habitats, ranging from soil collectives to the human microbiome. To function as productive communities, bacteria coordinate metabolic functions, often requiring shifts in growth and development. The hallmark of cellular development, which we characterize as physiological change in response to environmental stimuli, is a defining feature of many bacterial interspecies interactions. Bacterial communities rely on chemical exchanges to provide the cues for developmental change. Traditional methods in microbiology focus on isolation and characterization of bacteria in monoculture, separating the organisms from the surroundings in which interspecies chemical communication has relevance. Developing multispecies experimental systems that incorporate knowledge of bacterial physiology and metabolism with insights from biodiversity and metagenomics shows great promise for understanding interspecies chemical communication in the microbial world.

Lipid signaling in pathogenic fungi has been studied to determine the role of these pathways in fungal biology and human infections. Owing to their unique nature, they may represent targets for future antifungal treatments. Farnesol signaling was characterized as a quorum-sensing molecule, with exposure inhibiting filamentation. Research has shown involvement in both the Ras1-adenylate cyclase and MAP kinase pathways. In species of Aspergillus, farnesol exposure induces apoptosis-like changes and alterations in ergosterol synthesis. Eicosanoid production has been characterized in several pathogenic fungi, utilizing host lipids in some cases. The role in virulence is not known yet, but it may involve modulation of host lipids. Sphingolipid signaling pathways seem to center around the production of diacylglycerol in the formation of inositol phosphorylceramide. Diacylglycerol activates both melanin production through laccase and transcription of antiphagocytic protein, both of which are involved in virulence.

Two-component signal transduction based on phosphotransfer from a histidine protein kinase to a response regulator protein is a prevalent strategy for coupling environmental stimuli to adaptive responses in bacteria. In both histidine kinases and response regulators, modular domains with conserved structures and biochemical activities adopt different conformational states in the presence of stimuli or upon phosphorylation, enabling a diverse array of regulatory mechanisms based on inhibitory and/or activating protein-protein interactions imparted by different domain arrangements. This review summarizes some of the recent structural work that has provided insight into the functioning of bacterial histidine kinases and response regulators. Particular emphasis is placed on identifying features that are expected to be conserved among different two-component proteins from those that are expected to differ, with the goal of defining the extent to which knowledge of previously characterized two-component proteins can be applied to newly discovered systems.

The assembly of the ribosome, a complex molecular machine composed of RNA and protein, is a poorly understood process. Recent work has demonstrated that GTPases are likely to play key roles in the assembly of ribosomes in bacteria and eukaryotes. This review highlights several bacterial ribosome assembly GTPases (RA-GTPases) and discusses possible functions for these proteins in the biogenesis of individual ribosomal subunits and subunit joining. RA-GTPases appear to link various aspects of the cell cycle and metabolism with translation. How these RA-GTPases may coordinate these connections are discussed.

The importance of lateral gene transfer in genome evolution of microbial eukaryotes is slowly being appreciated. Acquisitions of genes have led to metabolic adaptation in diverse eukaryotic lineages. In most cases the metabolic genes have originated from prokaryotes, often followed by sequential transfers between eukaryotes. However, the knowledge of gene transfer in eukaryotes is still mainly based on anecdotal evidence. Some of the observed patterns may be biases in experimental approaches and sequence databases rather than evolutionary trends. Rigorous systematic studies of gene acquisitions that allow for the possibility of exchanges of all categories of genes from all sources are needed to get a more objective view of gene transfer in eukaryote evolution. It may be that the role of gene transfer in the diversification process of microbial eukaryotes currently is underestimated.

Plasmodium sporozoites are the product of a complex developmental process in the mosquito vector and are destined to infect the mammalian liver. Attention has been drawn to the mosquito stages and pre-erythrocytic stages owing to recognition that these are bottlenecks in the parasite life cycle and that intervention at these stages can block transmission and prevent infection. Parasite progression in the Anopheles mosquito, sporozoite transmission to the mammalian host by mosquito bite, and subsequent infection of the liver are characterized by extensive migration of invasive stages, cell invasion, and developmental changes. Preparation for the liver phase in the mammalian host begins in the mosquito with an extensive reprogramming of the sporozoite to support efficient infection and survival. Here, we discuss what is known about the molecular and cellular basis of the developmental progression of parasites and their interactions with host tissues in the mosquito and during the early phase of mammalian infection.

Cryptococcus neoformans is a pathogenic fungus responsible for severe opportunistic infections. The most prominent feature of this yeast is its elaborate polysaccharide capsule, a complex structure that is required for virulence. The capsule is intimately associated with the cell wall, which underlies the capsule and offers the organism strength and flexibility in potentially hostile environments. Both structures are primarily composed of polysaccharides, offering a glimpse of the tremendous variation inherent in natural carbohydrate structures and their multiple biological functions. The steps in cell wall and capsule biosynthesis and assembly pose fascinating questions of metabolism, enzymology, cell biology, and regulation; the answers have potential application to treatment of a deadly infection. This article reviews current knowledge of cryptococcal cell wall and capsule biosynthesis and outstanding questions for the future.

Mitochondria in malaria parasites have some unusual evolutionary and functional features. The drastic reduction in the size of their mitochondrial genome, encoding just three proteins, appears to have originated at the point of divergence of dinoflagellates and apicomplexan parasites from ciliates and may have accompanied the acquisition of plastids by the former. Unusual translational machinery as revealed by the highly fragmented mitochondrial ribosomal RNA genes also appears to have originated at this deflection point. Some of the biochemical properties of malarial mitochondria also appear to be unconventional. Although tricarboxylic acid cycle enzymes are encoded by the genome, they do not appear to be involved in the full oxidation of glucose to fuel mitochondrial ATP synthesis in the blood stages of malaria parasites. A critical role of the mitochondrial electron transport chain appears to be to serve pyrimidine biosynthesis. In spite of their minimal nature, Plasmodium mitochondria are attractive targets for antimalarial drugs.

Lactobacilli and bifidobacteria have traditionally been recognized as potential health-promoting microbes in the human gastrointestinal tract, which is clearly reflected by the pre- and probiotic supplements on the market. Bacterial genomics of lactobacilli and bifidobacteria is initiating the identification and validation of specific effector molecules that mediate host health effects. Combined with advanced postgenomic mammalian host response analyses, elucidations of the molecular interactions and mechanisms that underlie the host-health effects observed are beginning to be gathered. These developments should be seen in the complexity of the microbiota-host relationships in the intestine, which through the new metagenomic era has regained momentum and will undoubtedly progress to functional microbiomics and host response analyses within the next decade. Taken together, these developments are anticipated to dramatically alter the scope and impact of the probiotic field, offering tremendous new opportunities with accompanying challenges for research and industrial application.

Batrachochytrium dendrobatidis (Bd) is a chytrid fungus that causes chytridiomycosis in amphibians. Only named in 1999, Bd is a proximate driver of declines in global amphibian biodiversity. The pathogen infects over 350 species of amphibians and is found on all continents except Antarctica. However, the processes that have led to the global distribution of Bd and the occurrence of chytridiomycosis remain unclear. This review explores the molecular, epidemiological, and ecological evidence that Bd evolved from an endemic ancestral lineage to achieve global prominence via anthropogenically mediated spread. We then consider the major host and pathogen factors that have led to the occurrence of chytridiomycosis in amphibian species, populations, and communities.

Methane is the most abundant hydrocarbon in the atmosphere, and it is an important greenhouse gas, which has so far contributed an estimated 20% of postindustrial global warming. A great deal of biogeochemical research has focused on the causes and effects of the variation in global fluxes of methane throughout earth's history, but the underlying microbial processes and their key agents remain poorly understood. This is a disturbing knowledge gap because 85% of the annual global methane production and about 60% of its consumption are based on microbial processes. Only three key functional groups of microorganisms of limited diversity regulate the fluxes of methane on earth, namely the aerobic methanotrophic bacteria, the methanogenic archaea, and their close relatives, the anaerobic methanotrophic archaea (ANME). The ANME represent special lines of descent within the Euryarchaeota and appear to gain energy exclusively from the anaerobic oxidation of methane (AOM), with sulfate as the final electron acceptor according to the net reaction:

This review summarizes what is known and unknown about AOM on earth and its key catalysts, the ANME clades and their bacterial partners.

African trypanosomes are devastating human and animal pathogens. Trypanosoma brucei rhodesiense and T. b. gambiense subspecies cause the fatal human disease known as African sleeping sickness. It is estimated that several hundred thousand new infections occur annually and the disease is fatal if untreated. T. brucei is transmitted by the tsetse fly and alternates between bloodstream-form and insect-form life cycle stages that are adapted to survive in the mammalian host and the insect vector, respectively. The importance of the flagellum for parasite motility and attachment to the tsetse fly salivary gland epithelium has been appreciated for many years. Recent studies have revealed both conserved and novel features of T. brucei flagellum structure and composition, as well as surprising new functions that are outlined here. These discoveries are important from the standpoint of understanding trypanosome biology and identifying novel drug targets, as well as for advancing our understanding of fundamental aspects of eukaryotic flagellum structure and function.

This review focuses on interactions among plants, mycorrhizal fungi, and bacteria, testing the hypothesis whether mycorrhizas can be defined as tripartite associations. After summarizing the main biological features of mycorrhizas, we illustrate the different types of interaction occurring between mycorrhizal fungi and bacteria, from loosely associated microbes to endobacteria. We then discuss, in the context of nutritional strategies, the mechanisms that operate among members of the consortium and that often promote plant growth. Release of active molecules, including volatiles, and physical contact among the partners seem important for the establishment of the bacteria/mycorrhizal fungus/plant network. The potential involvement of quorum sensing and Type III secretion systems is discussed, even if the exact nature of the complex interspecies/interphylum interactions remains unclear.

Upstream open reading frames (uORFs) are frequently present in the 5′-leader regions of fungal mRNAs. They can affect translation by controlling the ability of ribosomes that scan from the mRNA 5′ end to reach the downstream genic reading frame. The translation of uORFs can also affect mRNA stability. For several genes, including Saccharomyces cerevisiae GCN4, S. cerevisiae CPA1, and Neurospora crassa arg-2, regulation by uORFs controls expression in response to specific physiological signals. The roles of many uORFs that are identified by genome-level approaches, as have been initiated for Saccharomyces, Aspergillus, and Cryptococcus species, remain to be determined. Some uORFs may have regulatory roles, while others may exist to insulate the genic reading frame from the negative impacts of upstream translation start sites in the mRNA 5′ leader.

An astonishing diversity of microorganisms thrives on our planet and their activities are fundamental for the functioning of all ecosystems including the human body. Consequently, detailed insights into the functions performed by microorganisms in their natural environment are required to understand human biology and the biology of the world around us and to lay the foundations for targeted manipulation of microbial communities. Isotope-labeling techniques combined with molecular detection tools are frequently used by microbial ecologists to directly link structure and function of microbial communities and to monitor metabolic properties of uncultured microbes at the single-cell level. However, only the recent combination of such techniques with Raman microspectroscopy or secondary ion mass spectrometry enables functional studies of microbes on a single-cell level by using stable isotopes as labels. This review provides an overview of these new techniques and their applications in microbial ecology, which allow us to investigate the ecophysiology of uncultured microbes to an extent that was unimaginable just a few years ago.