Biology subjects

Rahman, M. K.

Publications and source records attributed to Rahman, M. K..

9 recordsLinked to original sources

bioRxiv2026

In situ cryo-EM reveals how a flagellar motor transmits high torque

Bacterial flagellar motors are diverse rotary machines that require robust mechanical coupling to transmit torque across components with distinct architectures, yet how such coupling is achieved remains poorly understood. Here, we determine near-atomic in situ structures of the periplasmic flagellar motor in the Lyme disease spirochete Borrelia burgdorferi, revealing how an expanded rotor is mechanically coupled to the conserved rod through symmetry breaking and local remodeling of the rotor rod interface. Surprisingly, pentameric FrbA forms a split washer-shaped brace around the rotor rod junction, providing a second layer of mechanical reinforcement. Deletion of frbA destabilizes distal flagellar structures and impairs motility, particularly under increased viscous load. FrbA homologues are broadly distributed across spirochetes, suggesting a conserved mechanism for reinforcing high-torque flagellar motors. Together, these findings reveal how symmetry breaking couples an expanded rotor to a conserved driveshaft, while a molecular split washer reinforces this interface to enable robust torque transmission and motility.

microbiology↗

bioRxiv2026

FlcE latches onto the FliL-stator complex to turbocharge flagellar motility in Borrelia burgdorferi

Periplasmic flagella are essential for the distinctive morphology and motility of the Lyme disease spirochete Borrelia burgdorferi, and motility plays a critical role in its pathogenic lifestyle. These flagella are powered by specialized motors that contain a large spirochete-specific multiprotein collar complex, yet the molecular architecture and mechanisms underlying high-torque motility remain poorly understood. Here, we identify the tetratricopeptide repeat (TPR)-containing protein BB0298 as a previously unrecognized flagellar collar component and rename it FlcE. Loss of flcE results in altered morphology and nearly abolishes the spirochetes motility. Using cryo-electron tomography and biochemical analyses, we show that FlcE occupies a unique position within the collar where it surrounds the FliL-stator complex by binding to FliL and the collar protein FlcA. These findings support a model in which FlcE functions as a molecular "latch" that secures stator assemblies to sustain efficient torque generation. Notably, flcE is conserved across most motile members of the Spirochaetales and is located within the division and cell-wall (dcw) gene cluster. More broadly, the conservation of TPR-containing structural proteins across diverse bacterial flagellar systems suggests a general architectural principle whereby dedicated scaffolds reinforce stator complexes to maximize motor performance under high mechanical loads. ImportanceSpirochetal motility requires the stable engagement of torque-generating stator units, yet the mechanisms that secure these complexes have remained unknown. Here, we identify FlcE as a previously unrecognized collar protein that functions as a molecular latch by restraining the FliL-stator complex. Loss of FlcE destabilizes FliL-stator assemblies and severely impairs motility, demonstrating that peripheral scaffolding is essential for sustaining high torque output in the Lyme disease spirochete Borrelia burgdorferi. The conservation of tetratricopeptide repeat domains in FlcE and other bacterial flagellar proteins further suggests a broader mechanism in which specialized scaffolds anchor and stabilize stator complexes, enabling high torque generation. Because motility is a central virulence determinant in many pathogenic bacteria--including B. burgdorferi during transmission from the tick to the mammalian host and subsequent infection--defining the mechanistic role of FlcE provides important insight into the molecular basis of motility-driven pathogenesis and suggests new strategies for disrupting bacterial infection.

microbiology↗

bioRxiv2026

In-situ structure of the flagellar export apparatus in Borrelia burgdorferi

The transmembrane export apparatus is a conserved core of bacterial type III secretion systems, shared by the flagellum and injectisome. Powered by the proton-motive force (PMF), this machinery translocates protein substrates across the bacterial envelope to support motility and virulence. However, its assembly and operation within native membranes remain poorly understood. Here, using in-situ single-particle cryo-electron microscopy, we resolve near-atomic-resolution structures of the flagellar export apparatus within the periplasmic flagellar motor of the Lyme disease spirochete Borrelia burgdorferi. Structural and genetic analyses suggest that coordinated, stepwise assembly of the flagellar export apparatus and MS-ring drives local deformation of the cytoplasmic membrane through extensive protein-lipid-protein interactions, constructing a funnel-shaped conduit optimal for substrate translocation. In addition, a conserved hydrophilic pathway lies within core export protein FlhA, with key acidic residues essential for export activity and supporting PMF-driven substrate translocation. Together, these findings establish a mechanistic framework for export apparatus assembly and energy transduction, defining core principles of type III secretion.

microbiology↗

bioRxiv2025

Insights into the genetic diversity and population structure of prevalent Theileria orientalis in Bangladesh

Theileria orientalis, an obligatory intracellular blood protozoon, which causes the substantial economic losses to the cattle industry and is widely prevalent throughout Bangladesh. The study was aimed to assess the nationwide prevalence, genetic diversity and evolutionary divergence of T. orientalis parasites in Bangladesh analyzing bovine blood samples. The genetic characterization, haplotype network analysis and Codon-based evolutionary divergence was conducted by targeting the major piroplasm surface protein (MPSP) gene. The overall prevalence of T. orientalis was 63.75% (n = 800), as determined by MPSP-PCR across the eight divisions of Bangladesh with significant regional variation. Subsequent phylogenetic analysis showed that the query MPSP sequences were clustered into two genotypes namely 5 and 7. Genetic diversity indicated high haplotype and moderate nucleotide diversity but consistent with contrasting demographic and selective pressures across regions. The evolutionary divergence analysis revealed the complex genetic landscape of T. orientalis population which shaped by historical expansion, ongoing gene flow and localized diversification. The haplotype network analysis identified total 29 distinct haplotypes, highlighting substantial diversity within the two genotypes. These findings demonstrate the occurrence and genetic richness of T. orientalis in cattle of Bangladesh. Although the pathogenic impact could not be assessed in this study, the presence of diverse genotypes suggests a need for continued surveillance and future research to determine the clinical and economic relevance of this parasite.

molecular biology↗

bioRxiv2022

Molecular characterization of enolase from Haemaphysalis longicornis tick

Withdrawal StatementThe authors have withdrawn their manuscript owing to for more improvement in our research work and need to revise our manuscript. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.

molecular biology↗

bioRxiv2019

FastFeatGen: Faster parallel feature extraction from genome sequences and efficient prediction of DNA N6-methyladenine sites

N6-methyladenine is widely found in both prokaryotes and eukaryotes. It is responsible for many biological processes including prokaryotic defense system and human diseases. So, it is important to know its correct location in genome which may play a significant role in different biological functions. Few computational tools exist to serve this purpose but they are computationally expensive and still there is scope to improve accuracy. An informative feature extraction pipeline from genome sequences is the heart of these tools as well as for many other bioinformatics tools. But it becomes reasonably expensive for sequential approaches when the size of data is large. Hence, a scalable parallel approach is highly desirable. In this paper, we have developed a new tool, called FastFeatGen, emphasizing both developing a parallel feature extraction technique and improving accuracy using machine learning methods. We have implemented our feature extraction approach using shared memory parallelism which achieves around 10x speed over the sequential one. Then we have employed an exploratory feature selection technique which helps to find more relevant features that can be fed to machine learning methods. We have employed Extra-Tree Classifier (ETC) in FastFeatGen and performed experiments on rice and mouse genomes. Our experimental results achieve accuracy of 85.57% and 96.64%, respectively, which are better or competitive to current state-of-the-art methods. Our shared memory based tool can also serve queries much faster than sequential technique. All source codes and datasets are available at https://github.com/khaled-rahman/FastFeatGen.

bioinformatics↗

bioRxiv2019

Megacities as drivers of national outbreaks: the role of holiday travel in the spread of infectious diseases

Human mobility connects populations and can lead to large fluctuations in population density, both of which are important drivers of epidemics. Measuring population mobility during infectious disease outbreaks is challenging, but is a particularly important goal in the context of rapidly growing and highly connected urban centers in low and middle income countries, which can act to amplify and spread local epidemics nationally and internationally. Here, we combine estimates of population movement from mobile phone data for over 4 million subscribers in the megacity of Dhaka, Bangladesh, one of the most densely populated cities globally. We combine mobility data with epidemiological data from a household survey, to understand the role of population mobility on the spatial spread of the mosquito-borne virus chikungunya within and outside Dhaka city during a large outbreak in 2017. The peak of the 2017 chikungunya outbreak in Dhaka coincided with the annual Eid holidays, during which large numbers of people traveled from Dhaka to their native region in other parts of the country. We show that regular population fluxes around Dhaka city played a significant role in determining disease risk, and that travel during Eid was crucial to the spread of the infection to the rest of the country. Our results highlight the impact of large-scale population movements, for example during holidays, on the spread of infectious diseases. These dynamics are difficult to capture using traditional approaches, and we compare our results to a standard diffusion model, to highlight the value of real-time data from mobile phones for outbreak analysis, forecasting, and surveillance.

ecology↗

bioRxiv2019

Prefix Block-Interchanges on Binary and Ternary Strings

The genome rearrangement problem computes the minimum number of operations that are required to sort all elements of a permutation. A block-interchange operation exchanges two blocks of a permutation which are not necessarily adjacent and in a prefix block-interchange, one block is always the prefix of that permutation. In this paper, we focus on applying prefix block-interchanges on binary and ternary strings. We present upper bounds to group and sort a given binary/ternary string. We also provide upper bounds for a different version of the block-interchange operation which we refer to as the restricted prefix block-interchange. We observe that our obtained upper bound for restricted prefix block-interchange operations on binary strings is better than that of other genome rearrangement operations to group fully normalized binary strings. Consequently, we provide a linear-time algorithm to solve the problem of grouping binary normalized strings by restricted prefix block-interchanges. We also provide a polynomial time algorithm to group normalized ternary strings by prefix block-interchange operations. Finally, we provide a classification for ternary strings based on the required number of prefix block-interchange operations.

bioinformatics↗

bioRxiv2018

PhISCS - A Combinatorial Approach for Sub-perfect Tumor Phylogeny Reconstruction via Integrative use of Single Cell and Bulk Sequencing Data

Recent technological advances in single cell sequencing (SCS) provide high resolution data for studying intra-tumor heterogeneity and tumor evolution. Available computational methods for tumor phylogeny inference via SCS typically aim to identify the most likely perfect phylogeny tree satisfying infinite sites assumption (ISA). However limitations of SCS technologies such as frequent allele dropout or highly variable sequence coverage, commonly result in mutational call errors and prohibit a perfect phylogeny. In addition, ISA violations are commonly observed in tumor phylogenies due to the loss of heterozygosity, deletions and convergent evolution. In order to address such limitations, we, for the first time, introduce a new combinatorial formulation that integrates single cell sequencing data with matching bulk sequencing data, with the objective of minimizing a linear combination of (i) potential false negatives (due to e.g. allele dropout or variance in sequence coverage) and (ii) potential false positives (due to e.g. read errors) among mutation calls, as well as (iii) the number of mutations that violate ISA - to define the optimal sub-perfect phylogeny. Our formulation ensures that several lineage constraints imposed by the use of variant allele frequencies (VAFs, derived from bulk sequence data) are satisfied. We express our formulation both in the form of an integer linear program (ILP) and - for the first time in the context of tumor phylogeny reconstruction - a boolean constraint satisfaction problem (CSP) and solve them by leveraging state-of-the-art ILP/CSP solvers. The resulting method, which we name PhISCS, is the first to integrate SCS and bulk sequencing data under the finite sites model. Using several simulated and real SCS data sets, we demonstrate that PhISCS is not only more general but also more accurate than the alternative tumor phylogeny inference tools. PhISCS is very fast especially when its CSP based variant is used returns the optimal solution, except in rare instances for which it provides an optimality gap. PhISCS is available at https://github.com/haghshenas/PhISCS.

bioinformatics↗