Resolving environmental drivers of microbial community structure in Antarctic soils

Antarctic soils are extremely cold, dry, and oligotrophic, yet harbour surprisingly high bacterial diversity. The severity of environmental conditions has constrained the development of multi-trophic communities, and species richness and distribution is thought to be driven primarily by abiotic factors. Sites in northern and southern Victoria Land were sampled for bacterial community structure and soil physicochemical properties in conjunction with the US and New Zealand Latitudinal Gradient Project. Bacterial community structure was determined using a high-resolution molecular fingerprinting method for 80 soil samples from Taylor Valley and Cape Hallett sites which are separated by five degrees of latitude and have distinct soil chemistry. Taylor Valley is part of the McMurdo Dry Valleys, while Cape Hallett is the site of a penguin rookery and contains ornithogenic soils. The influence of soil moisture, pH, conductivity, ammonia, nitrate, total nitrogen and organic carbon on community structure was revealed using Spearman rank correlation, Mantel test, and principal components analysis. High spatial variability was detected in bacterial communities and community structure was correlated with soil moisture and pH. Both unique and shared bacterial community members were detected at Taylor Valley and Cape Hallett despite the considerable distance between the sites

Convex Constraint Decomposition of Circular Dichroism Curves of Proteins

A new algorithm, called convex analysis, has been developed to deduce the chiral contribution of the common secondary structures directly from experimental circular dichroism (CD) curves of a large number of proteins. The analysis is based on CD data reported by Yang et aU Test runs were performed on sets of artificial protein spectra created by the Monte Carlo technique using poly-u-Iysine based component spectra. Application of the decomposition algorithm for the created sets of spectra resulted in component spectra [B (2, i)] and weights [C (i, k)] with excellent Pearson correlation coefficients (r).2 The algori thm, independent of X-ray data, revealed that the CD spectrum of a given protein is composed of at least four independent sources of chirality. Three of the computed component curves show remarkable resemblance to the CD spectra of known protein secondary structures. This approach yields a significant improvement compared to the eigenvector analysis of Hennessey and Johnson." The new method is a useful tool not only in analyzing CD spectra but also in treating other decomposition problems where an additivity constraint is valid

Role of the N-terminal transmembrane domain in the endo-lysosomal targeting and function of the human ABCB6 protein.

ABCB6 is a homodimeric ATP-binding cassette (ABC) transporter present in the plasma membrane and in intracellular organelles. The intracellular localization of ABCB6 has been a matter of debate, as it has been suggested to reside in the mitochondria and the endo-lysosomal system. Using a variety of imaging modalities including confocal and electron microscopy we confirm the endo-lysosomal localization of ABCB6 and show that the protein is internalized from the plasma membrane through endocytosis, to be distributed to multivesicular bodies and lysosomes. In addition to the canonical nucleotide binding (NBD) and transmembrane domains (TMD), ABCB6 contains a unique N-terminal transmembrane domain (TMD0), which does not show sequence homology to known proteins. We investigated the functional role of these domains through the molecular dissection of ABCB6. We find that the folding, dimerization, membrane insertion and ATP binding/hydrolysis of the core ABCB6 complex devoid of TMD0 is preserved. However, in contrast to the full-length transporter, the core ABCB6 construct is retained at the plasma membrane, and does not appear in Rab5-positive endosomes. TMD0 is directly targeted to the lysosomes, without a passage to the plasma membrane. Collectively, our results reveal that TMD0 represents an independently folding unit, which is dispensable for catalysis, but has a crucial role in the lysosomal targeting of ABCB6

PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes

Motivation: PSORTb has remained the most precise bacterial protein subcellular localization (SCL) predictor since it was first made available in 2003. However, the recall needs to be improved and no accurate SCL predictors yet make predictions for archaea, nor differentiate important localization subcategories, such as proteins targeted to a host cell or bacterial hyperstructures/organelles. Such improvements should preferably be encompassed in a freely available web-based predictor that can also be used as a standalone program

How AlphaFold2 shaped the structural coverage of the human transmembrane proteome

Abstract AlphaFold2 (AF2) provides a 3D structure for every known or predicted protein, opening up new prospects for virtually every field in structural biology. However, working with transmembrane protein molecules pose a notorious challenge for scientists, resulting in a limited number of experimentally determined structures. Consequently, algorithms trained on this finite training set also face difficulties. To address this issue, we recently launched the TmAlphaFold database, where predicted AlphaFold2 structures are embedded into the membrane plane and a quality assessment (plausibility of the membrane-embedded structure) is provided for each prediction using geometrical evaluation. In this paper, we analyze how AF2 has improved the structural coverage of membrane proteins compared to earlier years when only experimental structures were available, and high-throughput structure prediction was greatly limited. We also evaluate how AF2 can be used to search for (distant) homologs in highly diverse protein families. By combining quality assessment and homology search, we can pinpoint protein families where AF2 accuracy is still limited, and experimental structure determination would be desirable

NGS of Virus-Derived Small RNAs as a Diagnostic Method Used to Determine Viromes of Hungarian Vineyards

As virus diseases cannot be controlled by traditional plant protection methods, the risk of their spread have to be minimized on vegetatively propagated plants, such as grapevine. Metagenomic approaches used for virus diagnostics offer a unique opportunity to reveal the presence of all viral pathogens in the investigated plant, which is why their application can reduce the risk of using infected material for a new plantation. Here we used a special branch, deep sequencing of virus-derived small RNAs, of this high-throughput method for virus diagnostics, and determined viromes of vineyards in Hungary. With NGS of virus-derived small RNAs we could detect not only the viruses tested routinely, but also new ones, which had never been described in Hungary before. Virus presence did not correlate with the age of the plantation, moreover phylogenetic analysis of the identified virus isolates suggests that infections are mostly caused by the use of infected propagating material. Our results, validated by other molecular methods, raised further questions to be answered before this method can be introduced as a routine, reliable test for grapevine virus diagnostics

New Structural Arrangement of the Extracellular Regions of the Phosphate Transporter SLC20A1, the Receptor for Gibbon Ape Leukemia Virus*

Infection of a host cell by a retrovirus requires an initial interaction with a cellular receptor. For numerous gammaretroviruses, such as the gibbon ape leukemia virus, woolly monkey virus, feline leukemia virus subgroup B, feline leukemia virus subgroup T, and 10A1 murine leukemia virus, this receptor is the human type III sodium-dependent inorganic phosphate transporter, SLC20A1, formerly known as PiT1. Understanding the critical receptor functionalities and interactions with the virus that lead to successful infection requires that we first know the surface structure of the cellular receptor. Previous molecular modeling from the protein sequence, and limited empirical data, predicted a protein with 10 transmembrane helices. Here we undertake the biochemical approach of substituted cysteine accessibility mutagenesis to resolve the topology of this receptor in live cells. We discover that there are segments of the protein that are unexpectedly exposed to the outside milieu. By using information determined by substituted cysteine accessibility mutagenesis to set constraints in HMMTOP, a hidden Markov model-based transmembrane topology prediction method, we now propose a comprehensive topological model for SLC20A1, a transmembrane protein with 12 transmembrane helices and 7 extracellular regions, that varies from previous models and should permit approaches that define both virus interaction and transport function