Annual Review of Microbiology - Volume 64, 2010

Following the introduction of fluorescent protein tags, the application of fluorescence microscopy in microbial cell biology has advanced the field dramatically. We now understand that bacterial cells are not simple bags of enzymes but have complex internal structures, and that specific intracellular organization plays an important role in a number of processes, including signal transduction. The quantitative nature and high temporal resolution of fluorescence microscopy make it particularly useful for studies of intracellular dynamic systems, such as signaling networks. Applications of fluorescence microscopy in signaling are not limited to studying localization. Several techniques allow researchers to follow real-time dynamics of protein interactions, at steady state or upon stimulation, and therefore to investigate signal propagation, amplification, and integration in the cell. Moreover, microscopy enables investigation of single-cell gene expression kinetics, bringing such concepts as cell individuality and robustness against stochasticity of gene expression to the forefront of signaling studies.

Bacterial microcompartments (BMCs) are organelles composed entirely of protein. They promote specific metabolic processes by encapsulating and colocalizing enzymes with their substrates and cofactors, by protecting vulnerable enzymes in a defined microenvironment, and by sequestering toxic or volatile intermediates. Prototypes of the BMCs are the carboxysomes of autotrophic bacteria. However, structures of similar polyhedral shape are being discovered in an ever-increasing number of heterotrophic bacteria, where they participate in the utilization of specialty carbon and energy sources. Comparative genomics reveals that the potential for this type of compartmentalization is widespread across bacterial phyla and suggests that genetic modules encoding BMCs are frequently laterally transferred among bacteria. The diverse functions of these BMCs suggest that they contribute to metabolic innovation in bacteria in a broad range of environments.

The discovery of mitochondrion-type genes in organisms thought to lack mitochondria led to the demonstration that hydrogenosomes share a common ancestry with mitochondria, as well as the discovery of mitosomes in multiple eukaryotic lineages. No examples of examined eukaryotes lacking a mitochondrion-related organelle exist, implying that the endosymbiont that gave rise to the mitochondrion was present in the first eukaryote. These organelles, known as hydrogenosomes, mitosomes, or mitochondrion-like organelles, are typically reduced, both structurally and biochemically, relative to classical mitochondria. However, despite their diversification and adaptation to different niches, all appear to play a role in Fe-S cluster assembly, as observed for mitochondria. Although evidence supports the use of common protein targeting mechanisms in the biogenesis of these diverse organelles, divergent features are also apparent. This review examines the metabolism and biogenesis of these organelles in divergent unicellular microbes, with a focus on parasitic protists.

Pneumocystis species are ascomycetous fungi that obligatorily dwell with no apparent ill effect in the lungs of normal mammals, but they become pathogenic when host defenses are compromised. Identified more than 100 years ago, these atypical fungi manifest characteristics that are unique within the Fungi, such as the lack of ergosterol, genetic complexity of surface antigens, and antigenic variation. Thought to be confined to the severely immunocompromised host, Pneumocystis spp. are being associated with new population niches owing to the advent of immunomodulatory therapies and increased numbers of patients suffering from chronic diseases. The inability to grow Pneumocystis spp. outside the mammalian lung has thwarted progress toward understanding their basic biology, but via the use of new genetic tools and other strategies, researchers are beginning to uncover their biological and genetic characteristics including a biphasic life cycle, significant metabolic capacities, and modulation of lifestyles.

Methane produced in the biosphere is derived from two major pathways. Conversion of the methyl group of acetate to CH4 in the aceticlastic pathway accounts for at least two-thirds, and reduction of CO2 with electrons derived from H2, formate, or CO accounts for approximately one-third. Although both pathways have terminal steps in common, they diverge considerably in the initial steps and energy conservation mechanisms. Steps and enzymes unique to the CO2 reduction pathway are confined to methanogens and the domain Archaea. On the other hand, steps and enzymes unique to the aceticlastic pathway are widely distributed in the domain Bacteria, the understanding of which has contributed to a broader understanding of prokaryotic biology.

Clustered regularly interspaced short palindromic repeats (CRISPRs) along with Cas proteins is a widespread system across bacteria and archaea that causes interference against foreign nucleic acids. The CRISPR/Cas system acts in at least two general stages: the adaptation stage, where the cell acquires new spacer sequences derived from foreign DNA, and the interference stage, which uses the recently acquired spacers to target and cleave invasive nucleic acid. The CRISPR/Cas system participates in a constant evolutionary battle between phages and bacteria through addition or deletion of spacers in host cells and mutations or deletion in phage genomes. This review describes the recent progress made in this fast-expanding field.

Burkholderia pseudomallei and Burkholderia mallei are closely related gram-negative bacteria that can cause serious diseases in humans and animals. This review summarizes the current and rapidly expanding knowledge on the specific virulence factors employed by these pathogens and their roles in the pathogenesis of melioidosis and glanders. In particular, the contributions of recently identified virulence factors are described in the context of the intracellular lifestyle of these pathogens. Throughout this review, unique and shared virulence features of B. pseudomallei and B. mallei are discussed.

Mycoplasma, a genus of pathogenic bacteria, forms a membrane protrusion at a cell pole. It binds to solid surfaces with this protrusion and then glides. The mechanism is not related to known bacterial motility systems, such as flagella or pili, or to conventional motor proteins, including myosin. We have studied the fastest species, Mycoplasma mobile, and have proposed a working model as follows. The gliding machinery is composed of four huge proteins at the base of the membrane protrusion and supported by a cytoskeletal architecture from the cell inside. Many flexible legs approximately 50 nm long are sticking out from the machinery. The movements generated by the ATP hydrolysis cell inside are transmitted to the “leg” protein through a “gear” protein, resulting in repeated binding, pull, and release of the sialylgalactose fixed on the surface by the legs. The gliding of Mycoplasma pneumoniae, a species distantly related to M. mobile, is also discussed.

Bacteria sense and respond to a wide range of physical and chemical signals. Central to sensing and responding to these signals are two-component systems, which have a sensor histidine kinase (SK) and a response regulator (RR) as basic components. Here we review the different molecular mechanisms by which these signals are integrated and modulate the phosphorylation state of SKs. Apart from the basic mechanism, which consists of signal recognition by the SK that leads to an alteration of its autokinase activity and subsequently a change in the RR phosphorylation state, a variety of alternative modes have evolved. The biochemical data available on SKs, particularly their molecular interactions with signals, nucleotides, and their cognate RRs, are also reviewed.

In the 1830s, iron bacteria were among the first groups of microbes to be recognized for carrying out a fundamental geological process, namely the oxidation of iron. Due to lingering questions about their metabolism, coupled with difficulties in culturing important community members, studies of Fe-oxidizing bacteria (FeOB) have lagged behind those of other important microbial lithotrophic metabolisms. Recently, research on lithotrophic, oxygen-dependent FeOB that grow at circumneutral pH has accelerated. This work is driven by several factors including the recognition by both microbiologists and geoscientists of the role FeOB play in the biogeochemistry of iron and other elements. The isolation of new strains of obligate FeOB allowed a better understanding of their physiology and phylogeny and the realization that FeOB are abundant at certain deep-sea hydrothermal vents. These ancient microorganisms offer new opportunities to learn about fundamental biological processes that can be of practical importance.

Light is one of the most important environmental factors for orientation of almost all organisms on Earth. Whereas light sensing is of crucial importance in plants to optimize light-dependent energy conservation, in nonphotosynthetic organisms, the synchronization of biological clocks to the length of a day is an important function. Filamentous fungi may use the light signal as an indicator for the exposure of hyphae to air and adapt their physiology to this situation or induce morphogenetic pathways. Although a yes/no decision appears to be sufficient for the light-sensing function in fungi, most species apply a number of different, wavelength-specific receptors. The core of all receptor types is a chromophore, a low-molecular-weight organic molecule, such as flavin, retinal, or linear tetrapyrrols for blue-, green-, or red-light sensing, respectively. Whereas the blue-light response in fungi is one of the best-studied light responses, all other light-sensing mechanisms are less well studied or largely unknown. The discovery of phytochrome in bacteria and fungi in recent years not only advanced the scientific field significantly, but also had great impact on our view of the evolution of phytochrome-like photoreceptors.