Phycochromes b and d: their occurrence in some phycoerythrocyanin-containing blue-green algae (cyanobacteria)

Abstract
Phycochromes b and d, two types of photoreversibly photochromic pigments previously extracted from the blue-green alga Tolypothrix distorta , which contains phycoerythrocyanin, have now been found in three Anabaena strains also containing phycoerythrocyanin. Tests for the presence of phycochromes b and d in a number of blue-green algae lacking phycoerythrocyanin have been negative. The possibility that phycochrome b-type absorbance changes are due to changes in the α-subunit of phycoerythrocyanin is discussed.     

Distribution and functions of TonB-dependent transporters in marine bacteria and environments: implications for dissolved organic matter utilization

Background

Bacteria play critical roles in marine nutrient cycles by incorporating and redistributing dissolved organic matter (DOM) and inorganic nutrients in the ocean. TonB-dependent transporter (TBDT) proteins allow Gram-negative bacteria to take up scarce resources from nutrient-limiting environments as well as siderophores, heme, vitamin B12, and recently identified carbohydrates. Thus, the characterization of TBDT distribution and functions is essential to better understand the contribution TBDT to DOM assimilation and its consequences on nutrient cycling in the environment.

Methodology/Principal Findings

This study presents the distribution of encoded known and putative TBDT proteins in the genomes of microorganisms and from the Global Ocean Survey data. Using a Lek clustering algorithm and substrate specificities, the TBDT sequences were mainly classified into the following three groups: (1) DOM transporters; (2) Siderophores/Vitamins transporters; and (3) Heme/Hemophores/Iron(heme)-binding protein transporters. Diverse TBDTs were found in the genomes of oligotroph Citromicrobium bathyomarinum JL354 and Citromicrobium sp JLT1363 and were highly expressed in the stationary phase of bacterial growth. The results show that the Gammaproteobacteria and the Cytophaga-Flavobacterium-Bacteroides (CFB) group bacteria accounted for the majority of the TBDT gene pool in marine surface waters.

Conclusions/Significance

The results of this study confirm the ecological importance of TBDTs in DOM assimilation for bacteria in marine environments owing to a wide range of substrate utilization potential in the ubiquitous Gammaproteobacteria and CFB group bacteria.     

Comparative structural analysis of TonB-dependent outer membrane transporters: implications for the transport cycle

TonB-dependent outer membrane transporters (TBDTs) transport organometallic substrates across the outer membranes of Gram-negative bacteria. Currently, structures of four different TBDTs have been determined by X-ray crystallography. TBDT structures consist of a 22-stranded beta-barrel enclosing a hatch domain. Structure-based sequence alignment of these four TBDTs indicates the presence of highly conserved motifs in both the hatch and barrel domains. The conserved motifs of the two domains are always in close proximity to each other and interact. We analyzed the very large interfaces between the barrel and hatch domains of TBDTs and compared their properties to those of other protein-protein interfaces. These interfaces are extensively hydrated. Most of the interfacial waters form hydrogen bonds to either the barrel or the hatch domain, with the remainder functioning as bridging waters in the interface. The hatch/barrel interfacial properties most resemble those of obligate transient protein complexes, suggesting that the interface is conducive to conformational change and/or movement of the hatch within the barrel. These results indicate that TBDTs can readily accommodate substantial conformational change and movement of their hatch domains during the active transport cycle. Also, these structural changes may require only modest forces exerted by the energy-coupling TonB protein upon the transporter.     

The occurrence of cyanobacteria in pulp and paper waste-treatment systems

Pulp and paper secondary waste-treatment systems in Brazil, Canada, New Zealand, and the U.S.A. contained dynamic cyanobacterial communities, some of which exceeded heterotrophic bacterial biomass. No other viable photoautotrophic populations were detected in the ponds. Regardless of geographical location, Oscillatoriales including Phormidium, Geitlerinema, and Pseudanabaena were the dominant taxa. As well, Chroococcus (Chroococcales) was an important genus in Brazil and New Zealand. The possible impact of cyanobacteria on waste-treatment efficiency deserves further study given their large biomass and diverse metabolic characteristics.     

真核生物锌转运体及其活性的调控

真核生物的锌内稳态是由其众多特异转运体协同转运来实现的。有两个锌转运体家族ZIP和CDF被相继发现。ZIP家族的主要功能是摄取锌,而CDF家族成员主要参与锌的外排及锌在细胞内的区室化以达到解毒或贮存的目的。锌可在转录水平和翻译水平调控两类转运体的活性以维持锌在细胞和生物体水平的内稳态。     

Changing expression patterns of TonB-dependent transporters suggest shifts in polysaccharide consumption over the course of a spring phytoplankton bloom

Algal blooms produce large quantities of organic matter that is subsequently remineralised by bacterial heterotrophs. Polysaccharide is a primary component of algal biomass. It has been hypothesised that individual bacterial heterotrophic niches during algal blooms are in part determined by the available polysaccharide substrates present. Measurement of the expression of TonB-dependent transporters, often specific for polysaccharide uptake, might serve as a proxy for assessing bacterial polysaccharide consumption over time. To investigate this, we present here high-resolution metaproteomic and metagenomic datasets from bacterioplankton of the 2016 spring phytoplankton bloom at Helgoland island in the southern North Sea, and expression profiles of TonB-dependent transporters during the bloom, which demonstrate the importance of both the Gammaproteobacteria and the Bacteroidetes as degraders of algal polysaccharide. TonB-dependent transporters were the most highly expressed protein class, split approximately evenly between the Gammaproteobacteria and Bacteroidetes, and totalling on average 16.7% of all detected proteins during the bloom. About 93% of these were predicted to take up organic matter, and for about 12% of the TonB-dependent transporters, we predicted a specific target polysaccharide class. Most significantly, we observed a change in substrate specificities of the expressed transporters over time, which was not reflected in the corresponding metagenomic data. From this, we conclude that algal cell wall-related compounds containing fucose, mannose, and xylose were mostly utilised in later bloom stages, whereas glucose-based algal and bacterial storage molecules including laminarin, glycogen, and starch were used throughout. Quantification of transporters could therefore be key for understanding marine carbon cycling.Subject terms: Water microbiology, Molecular ecology, Proteomics     

Amino acids and their transporters in the retina

This review provides an overview of the distributions, properties and roles of amino acid transport systems in normal and pathological retinal tissues and discusses the roles of specific identified transporters in the mammalian retina. The retina is used in this context as a vehicle for describing neuronal and glial properties, which are in some, but not all cases comparable to those found elsewhere an the brain. Where significant departures are noted, these are discussed in the context of functional specialisations of the retina and its relationship to adjacent supporting tissues such as the retinal pigment epithelium. Specific examples are given where immunocytochemical labelling for amino acid transporters may yield inaccurate results, possibly because of activity-dependent conformation changes of epitopes in these proteins which render the epitopes more or less accessible to antibodies.     

Laccases and their occurrence in prokaryotes

Laccases are copper-containing proteins that require O(2) to oxidize phenols, polyphenols, aromatic amines, and different non-phenolic substrates by one-electron transfer, resulting in the formation of reactive radicals. Although their specific physiological functions are not completely understood, there are several indications that laccases are involved in the morphogenesis of microorganisms (e.g., fungal spore development, melanization) and in the formation and/or degradation of complex organic substances such as lignin or humic matter. Owing to their high relative non-specific oxidation capacity, laccases are useful biocatalysts for diverse biotechnological applications. To date, laccases have been found only in eukaryotes (fungi, plants); however, databank searches and experimental data now provide evidence for their distribution in prokaryotes. This survey shows that laccase-like enzymes occur in many gram-negative and gram-positive bacteria. Corresponding genes have been found in prokaryotes that are thought to have branched off early during evolution, e.g., the extremely thermophilic Aquifex aeolicus and the archaeon Pyrobaculum aerophilum. Phylogenetically, the enzymes are members of the multi-copper protein family that have developed from small-sized prokaryotic azurins to eukaryotic plasma proteins.     

Methods to detect cyanobacteria and their toxins in the environment

Cyanobacteria blooms are since early times a cause for environmental concern because of their negative impact through the release of odors, water discoloration, and more dangerously through the release of toxic compounds (i.e. the cyanotoxins) that can affect both human and animal welfare. Surveillance of the aquatic ecosystems is therefore obligatory, and methods to achieve such require a prompt answer not only regarding the species that are producing the blooms but also the cyanotoxins that are being produced and/or released. Moreover, besides this well-known source of possible intoxication, it has been demonstrated the existence of several other potential routes of exposure, either for humans or other biota such as through food additives and in terrestrial environments (in plants, lichens, biological soil crusts) and the recognition of their harmful impact on less studied ecosystems (e.g. coral reefs). Nowadays, the most frequent approaches to detect toxic cyanobacteria and/or their toxins are the chemical-, biochemical-, and molecular-based methods. Above their particular characteristics and possible applications, they all bring to the environmental monitoring several aspects that are needed to be discussed and scrutinized. The end outcome of this review will be to provide newer insights and recommendations regarding the methods needed to apply in an environmental risk assessment program. Therefore, a current state of the knowledge concerning the three methodological approaches will be presented, while highlighting positive and negative aspects of each of those methods within the purpose of monitoring or studying cyanobacteria and their toxins in the environment.     

Vacuolar transporters and their essential role in plant metabolism

Following the unequivocal demonstration that plants contain at least two types of vacuoles, scientists studying this organelle have realized that the plant 'vacuome' is far more complex than they expected. Some fully developed cells contain at least two large vacuoles, with different functions. Remarkably, even a single vacuole may be subdivided and fulfil several functions, which are supported in part by the vacuolar membrane transport systems. Recent studies, including proteomic analyses for several plant species, have revealed the tonoplast transporters and their involvement in the nitrogen storage, salinity tolerance, heavy metal homeostasis, calcium signalling, guard cell movements, and the cellular pH homeostasis. It is clear that vacuolar transporters are an integrated part of a complex cellular network that enables a plant to react properly to changing environmental conditions, to save nutrients and energy in times of plenty, and to maintain optimal metabolic conditions in the cytosol. An overview is given of the main features of the transporters present in the tonoplast of plant cells in terms of their function, regulation, and relationships with the microheterogeneity of the vacuome.     

The seasonal occurrence of chroococcoid cyanobacteria at an Antarctic coastal site

Summary The chroococcoid cyanobacterium Synechococcus was found at 5 m depth at a site 6 km off the Antarctic coast where the water depth was 30 m. These cells reached a peak concentration of 140 cells ml^-1 in August at the time of maximum rate of development of seaice. They were accompanied in the water column by detritus consisting of diatom frustules and sediment particles. A smaller peak of abundance occurred at the time the sea-ice was breaking up. Cyanobacteria were seen only in very low numbers at one, and were absent at the other, of two deep water sampling sites. We propose that the two peaks of cyanobacterial abundance in the water column result from the suspension of a benthic population by ice crystals during the winter and their release from the sea-ice in summer.     

The occurrence of rapidly reversible non-photochemical quenching of chlorophyll a fluorescence in cyanobacteria

Cyanobacteria have previously been considered to differ fundamentally from plants and algae in their regulation of light harvesting. We show here that in fact the ecologically important marine prochlorophyte, Prochlorococcus, is capable of forming rapidly reversible non-photochemical quenching of chlorophyll a fluorescence (NPQf or qE) as are freshwater cyanobacteria when they employ the iron stress induced chlorophyll-based antenna, IsiA. For Prochlorococcus, the capacity for NPQf is greater in high light-adapted strains, except during iron starvation which allows for increased quenching in low light-adapted strains. NPQf formation in freshwater cyanobacteria is accompanied by deep Fo quenching which increases with prolonged iron starvation.     

Genome mining demonstrates the widespread occurrence of gene clusters encoding bacteriocins in cyanobacteria

Cyanobacteria are a rich source of natural products with interesting biological activities. Many of these are peptides and the end products of a non-ribosomal pathway. However, several cyanobacterial peptide classes were recently shown to be produced through the proteolytic cleavage and post-translational modification of short precursor peptides. A new class of bacteriocins produced through the proteolytic cleavage and heterocyclization of precursor proteins was recently identified from marine cyanobacteria. Here we show the widespread occurrence of bacteriocin gene clusters in cyanobacteria through comparative analysis of 58 cyanobacterial genomes. A total of 145 bacteriocin gene clusters were discovered through genome mining. These clusters encoded 290 putative bacteriocin precursors. They ranged in length from 28 to 164 amino acids with very little sequence conservation of the core peptide. The gene clusters could be classified into seven groups according to their gene organization and domain composition. This classification is supported by phylogenetic analysis, which further indicated independent evolutionary trajectories of gene clusters in different groups. Our data suggests that cyanobacteria are a prolific source of low-molecular weight post-translationally modified peptides.     

Magnesium transporters and their role in Al tolerance in plants

Magnesium (Mg) is an essential macronutrient for plant growth, which has diverse biological functions. However, little is known about the transport system of this nutrient in plants. In the genome of plants such as rice and Arabidopsis, there are homologues of bacterial Mg transporters (CorA) and some of them have been functionally characterized, but the physiological role of these transporters are poorly understood. On the other hand, Mg is able to alleviate Al toxicity in a number of plant species, but the mechanisms underlying this alleviation are not well understood. Recently, this alleviation has been associated with a Mg transporter in rice. In this paper, we present our opinions on Mg transporters, which are required for uptake, translocation, distribution and storage in plants. Possible mechanisms for Mg-mediated alleviation of Al toxicity are also discussed.     

Sugar transporters in plants and in their interactions with fungi

Sucrose and monosaccharide transporters mediate long distance transport of sugar from source to sink organs and constitute key components for carbon partitioning at the whole plant level and in interactions with fungi. Even if numerous families of plant sugar transporters are defined; efflux capacities, subcellular localization and association to membrane rafts have only been recently reported. On the fungal side, the investigation of sugar transport mechanisms in mutualistic and pathogenic interactions is now emerging. Here, we review the essential role of sugar transporters for distribution of carbohydrates inside plant cells, as well as for plant-fungal interaction functioning. Altogether these data highlight the need for a better comprehension of the mechanisms underlying sugar exchanges between fungi and their host plants.     

Exopolysaccharide-producing cyanobacteria and their possible exploitation: A review

Since the early 1950s, more than one hundred cyanobacterial strains,belonging to twenty different genera, have been investigated with regard tothe production and the released exocellular polysaccharides (RPS) into theculture medium. The chemical and rheological properties show that suchpolysaccharides are complex anionic heteropolymers, in about 80% casescontaining six to ten different monosaccharides and in about 90% casescontaining one or more uronic acids; almost all have non-saccharidiccomponents, such as peptidic moieties, acetyl, pyruvyl and/or sulphategroups. Based on such ingredients, cyanobacterial RPSs show promise asthickening or suspending agents, emulsifying or cation-chelating compoundsand the residual capsulated cyanobacterial biomass, following RPSextraction, could be an effective cation-chelating material. Indeed, wheneleven unicellular and filamentous RPS-producing cyanobacteria, selectedon the basis of the anion density of their RPSs and on the abundance oftheir outermost investments, were screened for their ability to removeCu²⁺ from aqueous solutions, a quick and most effective heavy metaladsorption was observed for the unicellular Cyanothece CE 4 and thefilamentous Cyanospira capsulata. These results suggest the possibilityto accomplish, through the exploitation of RPS-producing cyanobacteria,a multiproduct strategy to procure a wide range of biopolymers suited tovarious industrial applications, in addition to the residual biomass effectivein the recovery of heavy metals from polluted waters.